User: zhaolin20042008

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Posts by zhaolin20042008

<prev • 8 results • page 1 of 1 • next >
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How should analyze if a Transcription factor significant in one condition vs. another using centipede footprints?
... Hi, My ATAC-seq data (unstimulation vs. stimulation) has been peak called, differential analyzed using DESeq2. Then all the peaks were put in Centipede for TF footprint analysis. The 402 motifs were input and around 360 motifs yield the output file of post probability. Now I want to compare the P ...
tf binding footprints postpr atac-seq written 6 months ago by zhaolin2004200810
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Comment: C: failed to covert bed files to make it compatible with UCSC trackhub
... Thank you. I checked the line 2551396 of footprints_2.bed chr2 1999786 2e+06 ELF5 99.9799 + So change awk 'BEGIN {OFS="\t"} {print $1,int($2),int($3), $4}' footprints_2.bed |sort -k1,1 -k2,2n > new.footprints_2.bed ...
written 6 months ago by zhaolin2004200810
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failed to covert bed files to make it compatible with UCSC trackhub
... Hi, I have the 8 bed files footprints_1.bed, footprints_2.bed (sorted, and work well with other bedtools commander), like chrY 59017131 59017352 MAZ 99.9928 - chrY 59017132 59017353 MAZ 99.9989 - chrY 59017132 59017353 VEZF1 ...
bedtobigbed written 6 months ago by zhaolin2004200810 • updated 6 months ago by Pierre Lindenbaum126k
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Comment: C: Subsample BAM to fixed number of alignments
... I have tried the suggestion above with a little modification. My case is to sample 20 M reads each file on hundreds of bam files with replacement . The "[sample][1]" is the best tool. samtools view -o –h reads.sam reads.bam #with the good header sample -k 20000000 -r -p reads.sam > read ...
written 10 months ago by zhaolin2004200810
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Comment: C: Bam File: Change Chromosome Notation
... @Pierre I tried the code but something was not right. It really replaced '1' with "chr1". But next I failed to get the index file for the bam file. The error is "samtools index: file.bam is in a format that cannot be usefully indexed". I used samtools view -H to check @HD VN:1.3 SO:coordinate ...
written 12 months ago by zhaolin2004200810
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Comment: C: DiffBind update warnings and running errors
... Thanks for suggestion. I will try. ...
written 2.3 years ago by zhaolin2004200810
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DiffBind update warnings and running errors
... Hello, I have been working with DiffBind for 6 months. Recently I got some warnings when I update DiffBind 2.6.1. Then previously worked scripts failed to run in DiffBind 2.6.1. I reinstalled the older version 2.4.8 again,however, dba.count still failed if I chose score=DBA_SCORE_SUMMIT but works if ...
diffbind dba.count atac-seq written 2.3 years ago by zhaolin2004200810 • updated 2.3 years ago by Devon Ryan94k
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How could I input a folder of bed, bim, fam files with different chromsomes to plink as --bfile mydata?
... Hello, I am new in LD analysis. I have a snp list from different chromosomes and a list of regions (less than +/- 5000 bp to snps) for LD calculation. The1000g dataset is a folder including the bed, bim, fam files of different chromosomes, the prefix name is chrXX_EUR. How could I input the folde ...
snp plink input written 2.3 years ago by zhaolin2004200810

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